Here's a place where I can post my thoughts on new papers, provide updates on my projects, and post info that will eventually be on my website The Theropod Database - http://theropoddatabase.com/ . It will center on theropods, but may delve into other topics as well such as phylogenetics.

Saturday, May 24, 2014

Revisiting a BAND cladogram

Twelve years ago, I replied to a post Nick Gardner wrote to the DML, critiquing and updating the phylogenetic analysis of Hou et al. (1996). This was perhaps the first analysis that I corrected and reran, which is now the concept behind an entire section of my website. Well, now I've officially reexamined Hou et al.'s data for an entry in the Database.

To jog everyone's memory, Hou et al.'s paper provided details on Confuciusornis, Liaoningornis and Chaoyangia and was interesting in that it included a cladogram with matrix for birds, not before (or since?) done by the Birds Are Not Dinosaurs (BAND) crowd. This cladogram supported the BAND concept of Sauriurae including Confuciusornis and enantiornithines, and supposedly used Petrolacosaurus as an outgroup. Hou et al. claim "The
use of a coelurosaurian dinosaur like Velociraptor as the outgroup would
make no difference for character states." Really? The figured cladogram also oddly differed from the matrix in adding 'Modern Birds'
as sister to Ichthyornis and replacing Cathayornis with Enantiornithes. The figure has a similar but different character list than the matrix (note my old post dealt with the figure's character list, so the numbers don't match up with my new critique). The authors' phylogeny was-

Go here to read commentary on all of the characters and codings. This analysis is hindered by its small
size, several characters based on fictional morphologies, others that are the
opposite of other characters, and some which are based on developmental assumptions
that cannot be coded in adult specimens. This leaves only seventeen characters
that are valid and phylogenetically informative. The anatomy of Archaeopteryx
has been greatly misunderstood by BANDits for decades, which spread somewhat
to Confuciusornis. Hou et al. also ascribed unsupported referred specimens
to Cathayornis and Chaoyangia, negating many of the codings for
those taxa. Petrolacosaurus was coded 0 for everything, including characters
it actually has state 1 for, those which are unpreserved, and even those based
on structures it lacks. Ichthyornis
meanwhile was coded as if it were a complete ornithurine, despite not preserving
several elements. These examples show Hou et al. coded taxa as idealized hypothetical
examples instead of actual specimens. In total, 43% (110/256) of characters
were miscoded, though this is somewhat exaggerated by the several deleted characters.
Once corrected, the consensus is-

This differs from the original tree in having a paraphyletic 'Sauriurae', though
differs from the modern consensus in placing Confuciusornis closer to
Aves than enantiornithines. This is no doubt due to the low number of characters, and as noted on my site, changed with only 2 extra steps.
Liaoningornis moved to Enantiornithes, matching O'Connor's (2012) redescription. Hou et al.'s original flawed matrix finds Pygostylia and Ornithothoraces instead of Sauriurae with only 3 extra steps, so doesn't even support their own hypothesis strongly. Indeed, my conclusion is that the matrix is
too small to strongly reject any proposed hypothesis.

What about Petrolacosaurus?

It's very odd that Hou et al. would choose Petrolacosaurus as their avian outgroup. I mean, even BANDits think birds are archosaurs, so why not use Euparkeria or Ornithosuchus? As noted above, they state
"The use of a coelurosaurian dinosaur like Velociraptor as the outgroup
would make no difference for character states" compared to their supposed
use of Petrolacosaurus. Well let's check that.

If Velociraptor is added, there are in
fact nine characters that are coded differently. Velociraptor is known
to have feathers (based on ulnar quill knobs) whereas Petrolacosaurus'
integument is unpreserved though originally miscoded as known. Petrolacosaurus
is inapplicable for hypocleidium length, anterior sternal groove presence and
sternal length (all originally miscoded), due to lacking a furcula or ossified
sternum, unlike Velociraptor. Velociraptor has uncinate processes,
unlike Petrolacosaurus or even Archaeopteryx. Velociraptor
has an ectocondylar tuber on its femur like Archaeopteryx, though Hou
et al. view the latter's structure as a non-homologous structure. Petrolacosaurus'
pedal unguals are not enlarged (again miscoded by Hou et al.), but Velociraptor
has pedal ungual II enlarged so is polymorphic. Most amusingly, Petrolacosaurus
actually has a dorsolaterally grooved clavicle and proximodorsal ischial
process like some basal birds (but unlike Velociraptor), though Hou
et al. miscoded these in assuming it was a generic diapsid. That's right. The BANDits had data to support their hypothesis, but didn't realize it due to their own laziness and evolutionary assumption that these were derived sauriurine characters instead of symplesiomorphies.

1 comment:

In looking at your blog I have thought you and your readers might be interested in my company’s new app – Real World Dinosaurs – now available on the app store.

http://realworlddinosaurs.com

Though it isn't about therapods in particular - it’s more like an overview of information on different dinosaurs - I still think you guys could find it useful or even just fun. Plus there are beautiful animations of each dinosaur it covers and more dinosaurs will be added, too!

Anyway, I hope you’ll check it out. I am really impressed by all your blogging and wanted to pass on the info on our app.